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- PDB-3wx6: Crystal structure of Type Six Secretion System protein -

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Basic information

Entry
Database: PDB / ID: 3wx6
TitleCrystal structure of Type Six Secretion System protein
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Hexameric assembly / Hexameric ring / T6SS protein
Function / homologyType VI secretion system effector Hcp / Hcp1-like superfamily / Type VI secretion system effector, Hcp / Hcp protein
Function and homology information
Biological speciesBurkholderia pseudomallei K96243 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsJobichen, C. / Sivaraman, J.
CitationJournal: Sci Rep / Year: 2015
Title: Extended Loop Region of Hcp1 is Critical for the Assembly and Function of Type VI Secretion System in Burkholderia pseudomallei.
Authors: Lim, Y.T. / Jobichen, C. / Wong, J. / Limmathurotsakul, D. / Li, S. / Chen, Y. / Raida, M. / Srinivasan, N. / MacAry, P.A. / Sivaraman, J. / Gan, Y.H.
History
DepositionJul 17, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)38,0932
Polymers38,0932
Non-polymers00
Water82946
1
A: Uncharacterized protein
B: Uncharacterized protein
x 6


Theoretical massNumber of molelcules
Total (without water)228,55912
Polymers228,55912
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area38930 Å2
ΔGint-152 kcal/mol
Surface area49540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.738, 82.738, 64.782
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein Uncharacterized protein


Mass: 19046.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei K96243 (bacteria)
Strain: K96243 / Gene: BPSS1498, Hcp1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q63K67
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.68 Å3/Da / Density % sol: 26.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M NaHEPES, 1M tri-sodiumcitrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2012 / Details: Mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. all: 6995 / Num. obs: 6995 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 29.5 % / Rsym value: 0.115
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 29.5 % / Num. unique all: 6695 / Rsym value: 0.274 / % possible all: 99

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.7→14.937 Å / σ(F): 0 / Phase error: 31.1 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2846 690 9.86 %RANDOM
Rwork0.2487 ---
all0.2846 6695 --
obs0.2536 6695 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→14.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1718 0 0 46 1764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061741
X-RAY DIFFRACTIONf_angle_d1.2192330
X-RAY DIFFRACTIONf_dihedral_angle_d16.635644
X-RAY DIFFRACTIONf_chiral_restr0.044258
X-RAY DIFFRACTIONf_plane_restr0.004295
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 90 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.7013-2.9080.32341320.31841245
2.908-3.19710.32751380.29751245
3.1971-3.65170.26941370.25041254
3.6517-4.57080.25951420.21271260
4.5708-13.48770.28361410.23331273
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.093-0.0844-0.03080.06470.00030.1881-0.0423-0.02370.0788-0.13550.1268-0.18340.0043-0.05810.21750.1729-0.02510.05150.0988-0.0040.072125.152516.88473.1837
20.0475-0.02420.01140.0564-0.04620.0177-0.04050.097-0.04160.1337-0.07990.04640.1042-0.14930.00010.19150.0057-0.03160.2109-0.01210.163414.466716.193379.6535
30.130.0992-0.01270.30980.12250.13680.038-0.0791-0.02470.16780.17530.009-0.01530.11550.23650.155-0.02170.07170.10650.05030.193525.790316.013376.0561
40.1555-0.07420.18630.05970.00320.2081-0.1623-0.0639-0.00260.2437-0.1406-0.1654-0.26910.1876-0.14010.08570.00040.09920.11480.0210.130519.419617.1474.0696
50.03930.0345-0.01640.009-0.02210.0084-0.07610.15620.12260.01310.1544-0.0716-0.0830.03460.04910.15760.1664-0.0554-0.1025-0.0670.370627.156423.623456.0699
60.0015-0.0125-0.00370.00630.00210.01190.0879-0.2880.0201-0.1959-0.05790.09060.1239-0.1133-0.00050.2327-0.0495-0.09060.28760.00620.226421.672-0.56941.7238
70.03590.00620.0018-0.00430.0179-0.01060.03720.01520.0680.08640.04090.07270.053-0.11430.01380.1929-0.11010.063-0.12210.0790.419218.975814.826654.1459
80.0022-0.00060.00110.00010.0030.00650.01510.03680.0008-0.00390.0145-0.0101-0.00940.0760.01240.10870.0260.01430.2070.0850.260316.842326.115551.1329
90.00220.0032-0.0080.0012-0.0210.05580.11020.1271-0.1342-0.03050.0814-0.0821-0.04420.02110.0952-0.43050.0306-0.32320.1068-0.03140.250227.86316.557852.8774
100.1366-0.0516-0.15940.31110.02730.27180.06960.081-0.13720.1044-0.3724-0.0685-0.1320.4228-0.09890.11560.0815-0.0403-0.28270.19590.38426.693511.039551.2958
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 7:40 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 41:68 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 69:117 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 118:168 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 3:35 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 36:50 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 51:68 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 69:78 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 79:110 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 111:168 )

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